Human Gene HNRNPU (uc001iaz.1) Description and Page Index
  Description: Homo sapiens heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) (HNRNPU), transcript variant 1, mRNA.
RefSeq Summary (NM_031844): This gene encodes a member of a family of proteins that bind nucleic acids and function in the formation of ribonucleoprotein complexes in the nucleus with heterogeneous nuclear RNA (hnRNA). The encoded protein has affinity for both RNA and DNA, and binds scaffold-attached region (SAR) DNA. Mutations in this gene have been associated with epileptic encephalopathy, early infantile, 54. A pseudogene of this gene has been identified on chromosome 14. [provided by RefSeq, Jun 2017].
Transcript (Including UTRs)
   Position: hg19 chr1:245,013,602-245,027,827 Size: 14,226 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr1:245,017,752-245,027,609 Size: 9,858 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:245,013,602-245,027,827)mRNA (may differ from genome)Protein (825 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Heterogeneous nuclear ribonucleoprotein U; Short=hnRNP U; AltName: Full=Scaffold attachment factor A; Short=SAF-A; AltName: Full=p120; AltName: Full=pp120;
FUNCTION: Component of the CRD-mediated complex that promotes MYC mRNA stabilization. Binds to pre-mRNA. Has high affinity for scaffold-attached region (SAR) DNA. Binds to double- and single- stranded DNA and RNA.
SUBUNIT: Identified in the spliceosome C complex. Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and untranslated mRNAs. Interacts with IGF2BP1 and ERBB4. Ligand for CR2.
INTERACTION: P42771:CDKN2A; NbExp=2; IntAct=EBI-351126, EBI-375053;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Cell surface. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Component of ribonucleosomes. Also found associated with the cell surface.
PTM: Extensively phosphorylated.
PTM: Arg-733 and Arg-739 are dimethylated, probably to asymmetric dimethylarginine.
SIMILARITY: Contains 1 B30.2/SPRY domain.
SIMILARITY: Contains 1 SAP domain.
SEQUENCE CAUTION: Sequence=AAC19382.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HNRNPU
CDC HuGE Published Literature: HNRNPU
Positive Disease Associations: Parkinson Disease
Related Studies:
  1. Parkinson Disease
    Hon-Chung Fung et al. Lancet neurology 2006, Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data., Lancet neurology. [PubMed 17052657]
    We generated publicly available genotype data for Parkinsons disease patients and controls so that these data can be mined and augmented by other researchers to identify common genetic variability that results in minor and moderate risk for disease.

-  MalaCards Disease Associations
  MalaCards Gene Search: HNRNPU
Diseases sorted by gene-association score: epileptic encephalopathy, early infantile, 54* (930), 1q44 microdeletion syndrome* (25), diffuse gastric cancer (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 104.04 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2620.07 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -86.80218-0.398 Picture PostScript Text
3' UTR -1060.134150-0.255 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001870 - B30.2/SPRY
IPR008985 - ConA-like_lec_gl_sf
IPR003034 - SAP_DNA-bd
IPR018355 - SPla/RYanodine_receptor_subgr
IPR003877 - SPRY_rcpt

Pfam Domains:
PF00622 - SPRY domain
PF02037 - SAP domain
PF13671 - AAA domain

SCOP Domains:
68906 - SAP domain
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help


ModBase Predicted Comparative 3D Structure on Q00839
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000993 RNA polymerase II core binding
GO:0001047 core promoter binding
GO:0001097 TFIIH-class transcription factor binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0003725 double-stranded RNA binding
GO:0003727 single-stranded RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0003779 actin binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008143 poly(A) binding
GO:0017069 snRNA binding
GO:0017130 poly(C) RNA binding
GO:0031490 chromatin DNA binding
GO:0034046 poly(G) binding
GO:0036002 pre-mRNA binding
GO:0042802 identical protein binding
GO:0043021 ribonucleoprotein complex binding
GO:0043565 sequence-specific DNA binding
GO:0044877 macromolecular complex binding
GO:0070034 telomerase RNA binding
GO:0099122 RNA polymerase II C-terminal domain binding
GO:1990837 sequence-specific double-stranded DNA binding
GO:1990841 promoter-specific chromatin binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
GO:0000398 mRNA splicing, via spliceosome
GO:0001649 osteoblast differentiation
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0007049 cell cycle
GO:0007275 multicellular organism development
GO:0007346 regulation of mitotic cell cycle
GO:0008380 RNA splicing
GO:0009048 dosage compensation by inactivation of X chromosome
GO:0016070 RNA metabolic process
GO:0030154 cell differentiation
GO:0032211 negative regulation of telomere maintenance via telomerase
GO:0032922 circadian regulation of gene expression
GO:0033673 negative regulation of kinase activity
GO:0034244 negative regulation of transcription elongation from RNA polymerase II promoter
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048255 mRNA stabilization
GO:0048511 rhythmic process
GO:0051301 cell division
GO:0051457 maintenance of protein location in nucleus
GO:0055013 cardiac muscle cell development
GO:0070934 CRD-mediated mRNA stabilization
GO:0071385 cellular response to glucocorticoid stimulus
GO:0090336 positive regulation of brown fat cell differentiation
GO:1901673 regulation of mitotic spindle assembly
GO:1902275 regulation of chromatin organization
GO:1902425 positive regulation of attachment of mitotic spindle microtubules to kinetochore
GO:1902889 protein localization to spindle microtubule
GO:1990280 RNA localization to chromatin
GO:1990830 cellular response to leukemia inhibitory factor
GO:1990845 adaptive thermogenesis
GO:2000373 positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity
GO:2000648 positive regulation of stem cell proliferation
GO:2000737 negative regulation of stem cell differentiation

Cellular Component:
GO:0000228 nuclear chromosome
GO:0000775 chromosome, centromeric region
GO:0000776 kinetochore
GO:0000777 condensed chromosome kinetochore
GO:0000922 spindle pole
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005819 spindle
GO:0005856 cytoskeleton
GO:0009986 cell surface
GO:0016020 membrane
GO:0016363 nuclear matrix
GO:0016607 nuclear speck
GO:0030496 midbody
GO:0032991 macromolecular complex
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0070937 CRD-mediated mRNA stability complex
GO:0071013 catalytic step 2 spliceosome
GO:0072686 mitotic spindle
GO:0098577 inactive sex chromosome
GO:1990023 mitotic spindle midzone
GO:1990498 mitotic spindle microtubule
GO:1990904 ribonucleoprotein complex
GO:0005697 telomerase holoenzyme complex
GO:0090575 RNA polymerase II transcription factor complex

-  Descriptions from all associated GenBank mRNAs
  LP895192 - Sequence 56 from Patent EP3253886.
AK095525 - Homo sapiens cDNA FLJ38206 fis, clone FCBBF1000449.
BC015782 - Homo sapiens heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A), mRNA (cDNA clone MGC:23593 IMAGE:4857112), complete cds.
AK126868 - Homo sapiens cDNA FLJ44920 fis, clone BRAMY3011501, highly similar to Heterogeneous nuclear ribonucleoprotein U.
AK130669 - Homo sapiens cDNA FLJ27159 fis, clone SYN00850.
BC034925 - Homo sapiens, Similar to heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A), clone IMAGE:3953856, mRNA, partial cds.
BC007950 - Homo sapiens heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A), mRNA (cDNA clone IMAGE:4299389), partial cds.
BC003367 - Homo sapiens heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A), mRNA (cDNA clone MGC:5216 IMAGE:2900876), complete cds.
AF068846 - Homo sapiens scaffold attachment factor A (SAF-A) mRNA, complete cds.
X65488 - H.sapiens U21.1 mRNA.
JD180118 - Sequence 161142 from Patent EP1572962.
JD502042 - Sequence 483066 from Patent EP1572962.
JD045559 - Sequence 26583 from Patent EP1572962.
JD485951 - Sequence 466975 from Patent EP1572962.
JD527443 - Sequence 508467 from Patent EP1572962.
JD092939 - Sequence 73963 from Patent EP1572962.
JD565968 - Sequence 546992 from Patent EP1572962.
AF461014 - Homo sapiens unknown mRNA.
BC024767 - Homo sapiens heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A), mRNA (cDNA clone MGC:29899 IMAGE:4993703), complete cds.
AK297119 - Homo sapiens cDNA FLJ54020 complete cds, highly similar to Heterogeneous nuclear ribonucleoprotein U.
JD142776 - Sequence 123800 from Patent EP1572962.
BC003621 - Homo sapiens heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A), mRNA (cDNA clone MGC:1992 IMAGE:2966453), complete cds.
EU831468 - Synthetic construct Homo sapiens clone HAIB:100066497; DKFZo008F1017 heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) protein (HNRNPU) gene, encodes complete protein.
EU831555 - Synthetic construct Homo sapiens clone HAIB:100066584; DKFZo004F1018 heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) protein (HNRNPU) gene, encodes complete protein.
DQ893316 - Synthetic construct clone IMAGE:100005946; FLH196102.01X; RZPDo839D06154D heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) (HNRPU) gene, encodes complete protein.
DQ896631 - Synthetic construct Homo sapiens clone IMAGE:100011091; FLH196098.01L; RZPDo839D06153D heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) (HNRPU) gene, encodes complete protein.
AB384995 - Synthetic construct DNA, clone: pF1KB4877, Homo sapiens HNRNPU gene for heterogeneous nuclear ribonucleoprotein U, complete cds, without stop codon, in Flexi system.
AK307661 - Homo sapiens cDNA, FLJ97609.
D13413 - Homo sapiens mRNA for p120, partial cds.
JD336900 - Sequence 317924 from Patent EP1572962.
JD458221 - Sequence 439245 from Patent EP1572962.
JD458230 - Sequence 439254 from Patent EP1572962.
JD556245 - Sequence 537269 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q00839 (Reactome details) participates in the following event(s):

R-HSA-72103 Formation of pre-mRNPs
R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-72172 mRNA Splicing

-  Other Names for This Gene
  Alternate Gene Symbols: HNRPU, HNRPU_HUMAN, NM_031844, NP_114032, O75507, Q00839, Q8N174, Q96HY9, Q9BQ09, SAFA, U21.1
UCSC ID: uc001iaz.1
RefSeq Accession: NM_031844
Protein: Q00839 (aka HNRPU_HUMAN)
CCDS: CCDS31081.1, CCDS41479.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_031844.2
exon count: 14CDS single in 3' UTR: no RNA size: 6846
ORF size: 2478CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5156.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.